SMTL ID : 5dyf.1

The crystal structure of Aminopeptidase N in complex with N-benzyl-1,2-diaminoethylphosphonic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.293, H.297, E.316, Y.377 Ligands: 5HR.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.293, A:H.297, A:E.316, A:E.316

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.781, R.789, R.822 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.789 Water bridges: A:R.781, A:R.789 Salt bridges: A:R.781, A:R.822 SO4.3: 3 residues within 4Å: Chain A: R.636, L.640, R.688 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.688 Water bridges: A:R.636, A:R.688 Salt bridges: A:R.636 SO4.4: 3 residues within 4Å: Chain A: T.565, R.568, R.569 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.568, A:R.569 SO4.5: 1 residues within 4Å: Chain A: D.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.244 Water bridges: A:D.244 SO4.6: 2 residues within 4Å: Chain A: A.331, S.332 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.332, A:S.332 Water bridges: A:R.333, A:R.333 SO4.7: 2 residues within 4Å: Chain A: L.402, R.406 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.406 SO4.8: 3 residues within 4Å: Chain A: A.191, V.192, K.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.192 Water bridges: A:L.190, A:E.213 SO4.9: 2 residues within 4Å: Chain A: R.203 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.203 SO4.10: 2 residues within 4Å: Chain A: R.277, K.736 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.736, A:K.736 Salt bridges: A:R.277, A:K.736 SO4.11: 4 residues within 4Å: Chain A: Q.851, E.852, G.853, L.854 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.851, A:G.853, A:L.854

1 x 5HR: [(1R)-1-amino-2-(benzylamino)ethyl]phosphonic acid(Non-covalent)

5HR.12: 21 residues within 4Å: Chain A: M.103, Q.115, E.117, P.118, F.254, N.255, M.256, G.257, A.258, M.259, E.260, H.293, E.294, H.297, K.315, E.316, N.369, Y.372, Y.377, Q.818 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.115 Hydrogen bonds: A:E.117, A:A.258, A:A.258, A:K.315, A:Y.377 Water bridges: A:E.294

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 8 residues within 4Å: Chain A: T.199, R.203, V.205, Y.241, D.242, L.243, D.244 Ligands: SO4.9 No protein-ligand interaction detected (PLIP) GOL.14: 4 residues within 4Å: Chain A: N.485, R.486, E.521, A.522 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.522 GOL.15: 3 residues within 4Å: Chain A: T.280, T.282, W.712 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.282, A:W.712 Water bridges: A:T.280, A:T.280, A:T.280, A:T.282, A:N.680 GOL.16: 4 residues within 4Å: Chain A: F.176, D.242, W.299, R.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.303, A:R.303

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.17: 6 residues within 4Å: Chain A: D.22, L.23, H.24, K.35, S.36, R.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.22 pi-Cation interactions: A:R.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., The crystal structure of Aminopeptidase N in complex with N-benzyl-1,2-diaminoethylphosphonic acid. To Be Published

Release Date

2015-11-25

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N

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